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Detailed information for vg0615849876:

Variant ID: vg0615849876 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 15849876
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GATTTGGCAGCCTCAACTTCATCACCAACGACCTTGGCAAGATCTCTCTCCTTGACTCGGATTCAAACCAGTCGGGGAGAGACCAGGTCTCCGCGCCGTT[C/T]
GGTATTCCGAACTCGGCCGAAGCCTACTCCAAGATCATCTCTCCCGAGTCGGCTTCAAACCACTCGGACGAGATCCAATCTACTCCTCCGCGACCAAATC

Reverse complement sequence

GATTTGGTCGCGGAGGAGTAGATTGGATCTCGTCCGAGTGGTTTGAAGCCGACTCGGGAGAGATGATCTTGGAGTAGGCTTCGGCCGAGTTCGGAATACC[G/A]
AACGGCGCGGAGACCTGGTCTCTCCCCGACTGGTTTGAATCCGAGTCAAGGAGAGAGATCTTGCCAAGGTCGTTGGTGATGAAGTTGAGGCTGCCAAATC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.90% 6.10% 0.02% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 31.60% 68.40% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 82.30% 1.04% 0.00% NA
Intermediate  90 85.60% 14.40% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0615849876 C -> T LOC_Os06g27930.1 synonymous_variant ; p.Phe52Phe; LOW synonymous_codon Average:68.136; most accessible tissue: Zhenshan97 flag leaf, score: 86.673 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0615849876 NA 2.94E-11 mr1649 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0615849876 NA 2.34E-06 mr1735 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0615849876 4.04E-07 NA mr1750_2 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0615849876 5.38E-06 NA mr1987_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251